Yuan Jiao, Zhou Xiang, Xu Guoqiang, Xu Sanping, Liu Bang
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.
Front Genet. 2022 Aug 25;13:910521. doi: 10.3389/fgene.2022.910521. eCollection 2022.
Tongcheng (TC) pigs, distinguished by their superior meat quality, are a Chinese indigenous pig breed. Recently, the genetic resources of TC pigs are under tremendous threat due to the introduction of cosmopolitan pig breeds and African swine fever disease. To promote their management and conservation, the present study assessed genetic diversity and population structure of TC pigs using single nucleotide polymorphism (SNP) markers. A total of 26, 999 SNPs were screened from 51, 315 SNPs in 68 TC pigs. The multi-dimensional scaling (MDS) analysis and neighbor-joining tree revealed that all 68 pigs were from a purebred population. The effective population size decreased over time, and it was 96 prior to generation 20. Both linkage disequilibrium (LD) and neutrality test indicated a low selection of TC pigs with average LD value of 0.15 ± 0.23. Genetic diversity results exhibited a minor allele frequency (MAF) of 0.23, observed heterozygosity (H) of 0.32, expected heterozygosity (He) of 0.31, and nucleotide diversity (Pi) of 0.31. All these parameters indicated a remarkably high genetic diversity of TC pigs. Additionally, 184 runs of homozygosity (ROH) segments were detected from the whole genome of TC pigs with an average ROH length of 23.71Mb, ranging from 11.26Mb to 69.02 Mb. The highest ROH coverage was found on chromosome 1 (10.12%), while the lowest was on chromosome 18 (1.49%). The average inbreeding coefficients based on ROH (F) was 0.04%. Fourteen ROH islands containing 240 genes were detected on 9 different autosomes. Some of these 240 genes were overlapped with the genes related to biological processes such as immune function, reproduction, muscular development, and fat deposition, including , , , , , and these genes might be associated with such traits as meat quality and disease resistance in TC pigs. Taken together, population structure and genetic diversity results suggested that the TC pig represented a valuable genetic resource. However, TC pig breed conservation program remains to be further optimized to ensure adequate genetic diversity and avoid inbreeding depression. Our findings provide theoretical basis for formulating management and conservation strategies for TC pigs.
通城猪以其优良的肉质而闻名，是中国本土猪种。近年来，由于外来猪种的引入和非洲猪瘟病的影响，通城猪的遗传资源面临巨大威胁。为了促进其管理和保护，本研究利用单核苷酸多态性（SNP）标记评估了通城猪的遗传多样性和种群结构。从68头通城猪的51315个SNP中筛选出26999个SNP。多维尺度分析（MDS）和邻接树分析表明，所有68头猪均来自纯种群体。有效种群数量随时间下降，在第20代之前为96头。连锁不平衡（LD）和中性检验均表明通城猪的选择压力较低，平均LD值为0.15±0.23。遗传多样性结果显示，次要等位基因频率（MAF）为0.23，观察杂合度（H）为0.32，期望杂合度（He）为0.31，核苷酸多样性（Pi）为0.31。所有这些参数表明通城猪具有非常高的遗传多样性。此外，在通城猪的全基因组中检测到184个纯合片段（ROH），平均ROH长度为23.71Mb，范围从11.26Mb到69.02Mb。在第1号染色体上发现的ROH覆盖率最高（10.12%），而在第18号染色体上最低（1.49%）。基于ROH的平均近交系数（F）为0.04%。在9条不同的常染色体上检测到14个包含240个基因的ROH岛。这240个基因中的一些与免疫功能、繁殖、肌肉发育和脂肪沉积等生物过程相关的基因重叠，包括 、 和 ，这些基因可能与通城猪的肉质和抗病性等性状有关。综上所述，种群结构和遗传多样性结果表明通城猪是一种有价值的遗传资源。然而，通城猪品种保护计划仍有待进一步优化，以确保足够的遗传多样性并避免近亲繁殖衰退。我们的研究结果为制定通城猪的管理和保护策略提供了理论依据。
